I've moved to a new neighborhood and there's a forest nearby. Today, to get a better idea of all the trails, the dog and I wandered every trail we could find. I also has Sports Tracker on to see what a trace of the ramble might reveal.
The resolution of the GPS kept some paths that I walked over more than once from being overlaid, showing two parallel paths.
But, for me, it gives me an idea of all the paths I can walk there.
I've been spending a lot of time thinking about how to find, navigate, recombine, and contribute to ... what's out there, though mostly focused on science and the next generation of science 'publishing' (in quotes, since it'll be quite different from traditional publishing, more back in the hands of the scientists like in the old days).
A friend pointed me to this cool site called WikiProfessional, where they have these cool info navigators. A quick perusal suggests that they focus on the 'find' and 'navigate', though I think they also have a wee bit of 'contribute' through the addition of semantics as you navigate and annotate.
There are a ton of collaborators working on this and I dug a bit deeper into the main one, Knewco, It was on their pages that I stumbled upon the image to the right, about the Knowlet, trademarked, but spot on representing what knowledge really is: a concept with a cloud of facts, co-occurring items, with a few predicted concepts thrown in.
I like.
UPDATE: And here's a paper that goes into the details.
I like. A lot.
A while back I found out via the Twitter site that the Mars Phoenix Lander had a Twitter channel. I don't know, but maybe at the time it didn't seem to be an interesting stream, what, but I didn't follow.
Well, seems like Alex is following the Lander and re-tweeted the big news below. So, I went to see the stream and am very pleased with how well they are using the stream. Not only is the person doing the tweeting very funny, but she has been responding to questions and such.
This is an excellent way of using Twitter in a corporate setting.
Did I say corporate? Indeed, this is NASA using Twitter to send out updates for one of their programs. Someone who represents the Lander is the one Tweeting, so that's marketing communications to me. And companies can learn a lot by just following this stream.
Way to go NASA!
Link: Twitter / MarsPhoenix:
Are you ready to celebrate? Well, get ready: We have ICE!!!!! Yes, ICE, *WATER ICE* on Mars! w00t!!! Best day ever!! about 7 hours ago from web
Does Massachusetts need a stimulus in biotech? I don't think so. It's doing pretty well.
This bill sounds like a bone thrown to biotech biz leaders around the state. One person in the article below even uttered the p-word "pork".
Oink oink, indeed.
On the plus side, maybe I should be thinking of heading back. That's a lot of moolah to go around.
"I just remind you that it's the taxpayers that are paying. ... It's taxpayers' money, it doesn't grow on trees," he said.
Image from extrudedaluminiu
Kevin Kelly whipped up 9 rules for the Century of Neo-Biology (that label thrills me).
I reproduce them here, but you might want to head over to his post (link below) to leave other rules there too.
1) All rules in biology have exceptions.
2) Anything that can be done with organisms (including our own), will be done.
3) Every biological action invokes a biological reaction.
4) All inovations follow a one-way migration from enhancements to normalcy.
5) One person's biological ideal is another's horror.
6) Understanding is not necessary for use.
7) The tolerence for uncertainty goes up as death becomes certain.
8) The difference between 99% reliable and 100% reliable is God (or a million years of evolution).
9) Health care is finite resources applied to an infinite appetite.
from: Kevin Kelly -- The Technium
I left the following comment
0) Biology is messy
Some folks think biology behaves properly and regularly like electronics (which we all know is a passing fad). Go into any laboratory and you will see the modern-day alchemist repeating experiments that work one day and not the other, joking about the phases of the moon or position of the chairs.
Do I feel this way because it is so early in the neo-biology game? Am I just an old fuddy-duddy who learned biology in the previous century?
I think that's irrelevant. Digital electronics have distracted us from the analogue world, such that when we turn our attentions to biology, we've forgotten how to think in gradients, thresholds, probability, or chaotic flows in regulatory networks. Indeed, the biochemistry I learned and did was all about this and it's a thrilling way of doing things. I think those with strong digital sensibilities will have a hard time embracing the uncertainty and variability so common in biological systems.
Call me an optimist, but I think it's inevitable that Earth-folk will eventually be wandering over Mars. Eh, not sure if it will happen in my lifetime or in my children's. I'm taking a long term view on this.
But last night, one more entry has been made in the time line: NASA set down a lander in the Mars arctic region.
I had comletely forgotten about it until I noticed an article in the Boston Globe. When I went to the mission site I found out that landing was immanent (but on the middle of my night). Of course, being the geek that I am, when I woke up the next morning I flipped open the computer to see what images were to be seen.
The one below seemed most interesting. Note the scalloped pattern to the dirt. Alas, what I hate about this pics is the lack of scale. When the first rover pics came in, things looked big and daunting, only to find out that they were tiny rocks and such. Sigh.
Nonetheless, I find this all exciting.
Can someone please explain to me how and why Thompson Reuters Scientific has such a grip on scientific journal Impact Factors?
If you look at the list of various indexing services, you can see that they are all brushed aside for Thompson Reuters. It seems to me that unless a journal is indexed by Thompson Retuers, then it really is not considered to have any relevant impact on the scientific literature.
OK, so maybe these guys were anointed by the community to stand in as the über-authority index. I can deal with that. But, I think also there is an opportunity for an independent authority index, à la Technorati.
I think it just might be my natural inclination to suspect a single source of authority ranking. But I think it's more likely because I see so many tools available to measure impact that could be more responsive and maybe more granular than what the current system seems like to me.
I've started looking into this. People are coming up with alternatives. It also seems like Thompson Reuters realizes that they might lose a hold on their position.
Yeah, my brain has been munging on this lately.
Link to article that set off this brainwave: BioMed Central Blog : Orphanet Journal of Rare Diseases tracked by Thomson Reuters and set to receive first impact factor in June 2008
Orphanet Journal of Rare Diseases was recently accepted for tracking by Thomson Reuters. It is included in the ISI Web of Knowledge database and will receive its first impact factor this summer. We are delighted with this achievement, which confirms the prominence and reputation which Orphanet Journal of Rare Diseases has achieved in its field.
Link to recent journal article: Effectiveness of Journal Ranking Schemes as a Tool for Locating Information
As de Solla Price observed [3], the number of scientific journals and the number of papers published in those journals is increasing at an approximately exponential rate. The size and growth of the research literature places a tremendous burden on researchers—how are they to select what to browse, what to read, and what to cite from a large and quickly growing body of literature?
I've been reading about iGEM and the Registry of Standard Biological Parts. It's a component view of biology - that there are parts in biology that can be used much like electronic parts.
Eh, I know they don't think it's that simple, but it sure can be misleading what they are trying to do.
These folks are characterizing biological parts and creating a catalogue from which to plug and play and mix and match to create circuits that do something. They are looking to establish standards, construction tools, and some abstraction to make it easier to build synthetic systems. And that's all fine and good. It's like the early days of electronics. And they have done some amazing things, light replicating photography with bacteria, some cool circuits, and more.
But, in my biomedical-scientist eyes, I just wished they would think more than just creating digital circuits on analogue systems. Also, I feel that biology doesn't gate well, I mean, it's very non-linear and hard to do on-off 'mathematics' with biological components. And by trying to build digital stuff, they lose the value of analogue.
In short, I think the questions they are asking are not the right ones for the system.
And thinking back to Craig Venter, moving forward, synthetic biologists are going to have to think of analogue, of biological answers to questions. We are so accustomed to neat and clean binary fixes to things, but seem to forget that in biology, so much is probability, fuzziness, and selection, and failure is so much more nuanced.
I've designed many macromolecules and expression systems, grew all sorts of micro and macro organisms, and dealt with all sorts of biological systems. In so many ways, we were not far from the brewers of Mesopotamia, coaxing and praying for a healthy growth and production of the right enzymes.
Yet, we have had in the past 30 years, and even more so in the past 5, a deeper understanding of the mechanisms. But, we mustn't just translate that all into our digital minds, we need to think of these organisms and molecules on their terms.
When I was a grad student, my advisor was a physical chemist doing biochemistry. To him, DNA wasn't just A T C and G, but a chemical entity. I came out of there seeing proteins and DNA in a way that my molecular biologist colleagues did not, and a deeper understanding of the complex interactions in biological systems.
In the same way, synthetic biology is going to have to go beyond linear circuit building, but take advantage of the strength of these marvelous billion-year evolved systems.
Here's a video of Drew Endy, a leader in this field, putting synthetic biology in perspective:
BONUS: If you really get a kick out of visualizations, the Machinery of Life, by David Goodsell, is a really neat peek into the molecular world at the scale of proteins and bacteria.
I finally got to listen to the Long Now seminar by Craig Venter. And, wow, was it great.
If you've been a regular reader of mine, you know that I think Venter deserves the Nobel many times over. He's been the big disruptor in genomics for decades, taking technological risks that made the industry jump forward farther than our prejudices would have expected.
The talk followed a thread through his disruptions, providing a foundation for why he's doing what he's doing now, which is to define the genome of an organism for practical purposes, such as creating biofuel.
One thing that he made me think about was bacteriology. When I was a scientist, we studied mammalian genes, proteins, and diseases. A bacteriologist always felt like someone from the distant past, with a lab full of smelly slimy plates, studying a 'boring' organism. A real microbiologist was studying fungi, like brewer's yeast, the laboratory workhorse and a model system for mammalian genetic and cellular processes.
Well, after listening to Venter, and aligning my perspective with his, it's clear that bacteriology is the domain to be in.
His recent Sorcerer II expedition has re-ignited interest in bacteria and bacterial ecology. With the recent rise in metabolomics (the analysis of all the metabolites in the body), we're starting to realize that our mammalian cells are an even smaller part of the body functions we have than we previously suspected. And as, I hope, the antibiotic era starts to wind down and people start redefining our relationship with bacteria, understanding bacteria has become ever more important.
That makes me think that the kinds of professions that will be on the rise in the post-genomic age are bacterial ecology, bacterial genomics, bacterial virology (phage therapy to replace antibiotics, is a new one for me), and bacterial biochemisty.
Questions I now would like to see answered: what are there bacteria who are exclusive inhabitants of humans, what is the total genomic signature of a human (the sum of human and microbiological), how can we live in a sceptic world (the rise of super-bugs is partly a consequence of our cleanliness).
I don't know if it's just me, but it seems like there's been a phase shift in biology on the order of the early days of molecular biology, with the excitement and promise of a very interesting future.
BONUS: One thing that I heard about that was intriguing was the Personal Genomics project, an open source community kind of project to not only get more genomes to sequence and analyze but also to drive the technology to cheaply sequence genomes (see X Prize, too). Indeed, I've been reading about the biological parts registry and wondering weather we are at a stage of garage molecular biology. But that's a later post. :-)
Heh. My Dad also had some of these types of clunker calculators. Uh, I was curious to see how it worked and opened it and, well, destroyed the whole thing. It was expensive, but my Dad was kind.
Funny, also, to see these photos today. Earlier I was wondering what would be the 'steampunk' version of my grandchildren's generations, as they look back at how backwards were were.
What got me thinking was a segment from Science Friday about folks who are reviving a pre-antibiotic anti-bacterial treatment (bacteriophage).
It also dovetalis with a recurring thought of setting up a bio-lab at home and trying to remember all I learned about early genetics labs and such. That's my 'steampunk' - milk bottles with fruit flies (I used to use them), capillary tubes with rubber hoses to measure microliters, funky autoclaves, light microscopes, different stains, and ... ah, it's so cool.
